Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_073037934.1 BUB04_RS06025 ABC transporter ATP-binding protein
Query= uniprot:D4GP38 (383 letters) >NCBI__GCF_900129305.1:WP_073037934.1 Length = 365 Score = 262 bits (669), Expect = 1e-74 Identities = 153/362 (42%), Positives = 214/362 (59%), Gaps = 23/362 (6%) Query: 3 QIQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYI 62 QI++ D+ K +G AV +S +++ + LV++GPSGCGK+T LR++AGLE TSG I+I Sbjct: 2 QIEIRDVRKDYGRVQAVRGVSFSVEEGQLLVILGPSGCGKTTLLRLIAGLEPVTSGTIHI 61 Query: 63 GGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETL 122 G + + P R+I+MVFQ YAL+PH+ VR+NI FGL+ + + E + R+ V + L Sbjct: 62 AGTDVTHLPPVKRNISMVFQSYALFPHLNVRENIIFGLKVRK-VPADEIERRLKRVVDLL 120 Query: 123 GIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQD 182 G++ LD KP ELSGG QQRVALGRAI+ + V LMDEPLSNLDAKLR MR E+ +LQ Sbjct: 121 GLSGRLDSKPGELSGGMQQRVALGRAIIAEKPVTLMDEPLSNLDAKLRNSMRREICSLQR 180 Query: 183 QLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMINL 242 +L +T +YVTH+Q EAMTMADRI +M DG++ Q SP Y P N FVA FIG P +N+ Sbjct: 181 RLGITMIYVTHDQVEAMTMADRIVLMRDGQIVQDDSPENFYERPANTFVARFIGTPPMNI 240 Query: 243 VRGTRSESTFVGEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVADAAPDDAALDDHDLQ 302 V ++ E L + D D ++ G+RPE++ +A++ L Sbjct: 241 VPLCPTQGGAALEPGGRLLFPGM-----DPDRYLFGIRPENLRLAESGQPAMVTGREYLG 295 Query: 303 MDVTV-VEPHGDQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTVTIPPDKIHLFDA 361 D V E HG + ++ T G + G V +T P ++LFDA Sbjct: 296 SDTFVSCEIHGQEVIVR----------------TRGRRNIREGTVVHLTWDPGDVNLFDA 339 Query: 362 ET 363 T Sbjct: 340 RT 341 Lambda K H 0.317 0.135 0.386 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 344 Number of extensions: 14 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 383 Length of database: 365 Length adjustment: 30 Effective length of query: 353 Effective length of database: 335 Effective search space: 118255 Effective search space used: 118255 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory